How to add/remove links to existing or new nodes using Python?
Since the name/labels of the nodes are all the same for all my objects I can simply use the same code for all other objects and it works. Here's how to do this automatically:

for mat in bpy.context.scene.objects.active.data.materials:
    for node in mat.node_tree.nodes:
        if node.label == "Mix Color/Alpha":
            if node.inputs[1].default_value[0] &lt; 1:
                mixColorAlphaNode = node
                for n in mat.node_tree.nodes:
                    if n.label == "Alpha BSDF":
                        alphaBSDFNode = n
                    elif n.label == "Shader Add Refl":
                        shaderAddReflNode = n
                    elif n.label == "Material Out":
                        materialOutNode = n

                # Math node
                mat.node_tree.nodes.new('ShaderNodeMath')
                mathNode = mat.node_tree.nodes[len(mat.node_tree.nodes)-1]
                mathNode.operation = 'LESS_THAN'
                mathNode.inputs[1].default_value = 1.0

                # Mix shader node
                mat.node_tree.nodes.new('ShaderNodeMixShader')
                mixShaderNode = mat.node_tree.nodes[len(mat.node_tree.nodes)-1]

                # Add links
                mat.node_tree.links.new(mathNode.outputs['Value'], mixShaderNode.inputs[0])
                mat.node_tree.links.new(mixColorAlphaNode.outputs[0], mathNode.inputs[0])
                mat.node_tree.links.new(mixColorAlphaNode.outputs[0], mathNode.inputs[0])
                mat.node_tree.links.new(shaderAddReflNode.outputs[0], mixShaderNode.inputs[1])
                mat.node_tree.links.new(alphaBSDFNode.outputs[0], mixShaderNode.inputs[2])
                mat.node_tree.links.new(mixShaderNode.outputs[0], materialOutNode.inputs[0])